I'd like to know what you think it's the best way to convert a level from "daylight" to night?
I was wondering if I should use a simple gradient and animate it's transparency but I don't know any other solution to do this.

I've never actually played Tiny Wings (gasp! I know, I really should), but what I would suggest is to play around in Photoshop or GIMP. Start with a screenshot, or a layered version of a scene and figure out what you can do to it using simple tints, overlays, etc that you can do to make it look night like. As long as you stick to operations that are easy to perform on the GPU, it's pretty easy to "port" the effect from an image editor into code.

That's what I've done in the past for figuring out how to do effects like that anyway.